Changes

Ri_zm calc (Part 2) - Move the brunt_vaisala smoothing into calc_brunt_vaisala_freq_sqd (#1156)

CLUBB ticket #1145

Includes previous steps:
* First step: Move call to calc_bv
* Ri_zm calc (Part 1.5) - Adjusted signature of diagnose_Lscale_from_tau #1145

Newest changes: Ri_zm calc (Part 2) - Move brunt_vaisala smoothing into calc_brunt_vaisala_freq_sqd

`brunt_vaisala_frq_sqd_smth` is now calculated in subroutine `calc_brunt_vaisala_freq_sqd` and it is now written to disk in `advance_clubb_core` with all the other `brunt_vaisala` variables.

Unfortunately, I had to make a couple more changes since moving this calculation into `calc_brunt_vaisala_freq_sqd` meant that any subroutine involved in calling `calc_stability_correction` would need to get `l_modify_limiters_for_cnvg_test` fed in, because `calc_brunt_vaisala_freq_sqd` is also called in `calc_stability_correction`.

This commit is BIT_CHANGING since `brunt_vaisala_frq_sqd_smth` used to be all zeros before this change in Lscale mode and now it is actually calculated. BFB in taus code.

Testing the new module system with our GPU diffness test. See https://github.com/larson-group/sys_admin/issues/829

The module system is setup via paths in /etc/profile.d/larson-group.sh, so we need to source it. https://github.com/larson-group/sys_admin/issues/829

Fixing bug in jenkinsfiles.